Overview


Site-level quality filters


Number of variant sites removed by each filter

The left panel shows counts of variant sites removed by individual filters, and the right panel shows counts of variant sites removed by all combinations of filters.


Pre-filter statistics

Variant counts for each strain based on vcf containing all variant sites called by GATK (“soft-filter.vcf”).


Post-filter statistics

Variant count for each strain based on the VCF containing only sites pass all filters (“hard-filter.vcf”). All heterozygous sites on main chromosomes were converted to either homozygous or missing. The remaining heterozygous sites are all located on mitochondria chromosomes.